We have been docking small molecules (e.g., drugs) into proteins using Monte Carlo (MC) simulation. The binding of a flavonoid inhibitor to cyclin dependent kinase 2 serves as a model system to investigate the reliability of computer simulations that allow both the protein and ligand to be flexible. In the absence of a crystal structure of the complex, such flexibility must be reliably handled to optimize drugs for proteins. In addition, a variety of programs were applied to docking problems to identify strengths and weaknesses of different software packages.Molecular modeling was used to assess the structural requirements for catalysis and dimerization of human methionine adenosyltransferase I/III. A manuscript was submitted for publication.Molecular modeling was also used to compare the amino acid presentation in the combining site between two anti-yeast iso-1 cytochrome c monoclonal antibodies whose epitopes are closely related. A manuscript was submitted for publication.The tetrameric state of the short coiled coil domain of the ORFIII product of cauliflower mosaic virus has been determined by several experimental methods. The 3D structure of the coiled coil tetramer was modeled in order to understand the structural principles of the alpha-helical coiled coil oligomerization. Several amino acid mutations were introduced into the coiled coil fragment based on the analysis of the modeled structure. The mutant structures were experimentally analyzed. A manuscript was submitted for publication.